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(-) Description

Title :  CRYSTAL STRUCTURE OF RUBISCO-LIKE PROTEIN FROM BACILLUS CEREUS ATCC 14579
 
Authors :  A. A. Fedorov, E. V. Fedorov, H. J. Imker, S. K. Burley, J. A. Gerlt, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  15 Dec 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Rubisco-Like Protein. Nysgxrc, Target 9463A, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Amino-Acid Biosynthesis, Isomerase, Magnesium, Metal-Binding, Methionine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Fedorov, E. V Fedorov, H. Imker, S. K. Burley, J. A. Gerlt, S. C. Almo
Crystal Structure Of Rubisco-Like Protein From Bacillus Cereus Atcc 14579
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RUBISCO-LIKE PROTEIN
    Chains: A, B
    EC Number: 5.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MTNW, BC_4036
    Organism Scientific: BACILLUS CEREUS ATCC 14579
    Organism Taxid: 226900
    Synonym: DK-MTP-1-P ENOLASE, RLP, 2,3-DIKETO-5- METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3FK4)

(-) Sites  (0, 0)

(no "Site" information available for 3FK4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FK4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3FK4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FK4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FK4)

(-) Exons   (0, 0)

(no "Exon" information available for 3FK4)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:388
 aligned with MTNW_BACCR | Q819E8 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:404
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402    
           MTNW_BACCR     3 GIIATYLIHDDSHNLEKKAEQIALGLTIGSWTHLPHLLQEQLKQHKGNVIHVEELAEHEHTNSYLRKKVKRGIIKIEYPLLNFSPDLPAILTTTFGKLSLDGEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVHDRPLLMSIFKGMIGRNIGYLKTQLRDQAIGGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGRTFDLKENAKRAVQAGADILLFNVFAYGLDVLQSLAEDDEIPVPIMAHPAVSGAYSASKLYGVSSPLLLGKLLRYAGADFSLFPSPYGSVALEKEEALAISKYLTEDDASFKKSFSVPSAGIHPGFVPFIVRDFGKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEVDDINLHSALQIWG 406
               SCOP domains d3fk4a1 A:3-121 automated mat          ches                                                                            d3fk4a2 A:122-406 automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhhhh...----------..hhhhh.eeeeeee...hhhhhhhhh...eeeeeeeeehhhhh..hhhhhhhhhhhhhhhh..eeeeeeeehhhhhh......hhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee...........hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh......eee....hhhhhh......hhhhhhhhhhhhhh..eeeee...------hhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eee.hhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fk4 A   3 GIIATYLIHDDSHNLEKKAEQIALGLTIG----------EQLKQHKGNVIHVEELAEHEHTNSYLRKKVKRGIIKIEYPLLNFSPDLPAILTTTFGKLSLDGEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVHDRPLLMSIFKGMIGRNIGYLKTQLRDQAIGGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGRTFDLKENAKRAVQAGADILLFNVFAYGLDVLQSLAEDDEIPVPIMAHPAVSGAYSASKLYGVSSPLLLGKLLRYAGADFSLFPSPY------KEEALAISKYLTEDDASFKKSFSVPSAGIHPGFVPFIVRDFGKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEVDDINLHSALQIWG 406
                                    12        22        |-        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302 |     312       322       332       342       352       362       372       382       392       402    
                                                       31         42                                                                                                                                                                                                                                                                   304    311                                                                                               


Chain B from PDB  Type:PROTEIN  Length:391
 aligned with MTNW_BACCR | Q819E8 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:404
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402    
           MTNW_BACCR     3 GIIATYLIHDDSHNLEKKAEQIALGLTIGSWTHLPHLLQEQLKQHKGNVIHVEELAEHEHTNSYLRKKVKRGIIKIEYPLLNFSPDLPAILTTTFGKLSLDGEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVHDRPLLMSIFKGMIGRNIGYLKTQLRDQAIGGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGRTFDLKENAKRAVQAGADILLFNVFAYGLDVLQSLAEDDEIPVPIMAHPAVSGAYSASKLYGVSSPLLLGKLLRYAGADFSLFPSPYGSVALEKEEALAISKYLTEDDASFKKSFSVPSAGIHPGFVPFIVRDFGKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEVDDINLHSALQIWG 406
               SCOP domains d3fk4b1 B:3-121 automated mat    ches                                                                                  d3fk4b2 B:122-406 automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee...hhhhhhhhhhhhh...----.hhhhhhhhhhhh.eeeeeee...hhhhhhhhh...eeeeeeeeehhhhh..hhhhhhhhhhhhhhhh..eeeeeeeehhhhhh......hhhhhhhhhhh.....eeeee.......hhhhhhhhhhhhhhh...eee......---..hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhh......eee....hhhhhh......hhhhhhhhhhhhhh..eeeee...------hhhhhhhhhhhhh........eeeee...hhhhhhhhhhhhh...eee..hhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fk4 B   3 GIIATYLIHDDSHNLEKKAEQIALGLTIG----LPHLLQEQLKQHKGNVIHVEELAEHEHTNSYLRKKVKRGIIKIEYPLLNFSPDLPAILTTTFGKLSLDGEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVHDRPLLMSIFKGMIGRNIGYLKTQLRDQAIGGVDIVKDDEILF---LTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGRTFDLKENAKRAVQAGADILLFNVFAYGLDVLQSLAEDDEIPVPIMAHPAVSGAYSASKLYGVSSPLLLGKLLRYAGADFSLFPSPY------KEEALAISKYLTEDDASFKKSFSVPSAGIHPGFVPFIVRDFGKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEVDDINLHSALQIWG 406
                                    12        22        |-   |    42        52        62        72        82        92       102       112       122       132       142       152       162       172       | - |     192       202       212       222       232       242       252       262       272       282       292       302 |     312       322       332       342       352       362       372       382       392       402    
                                                       31   36                                                                                                                                             180 184                                                                                                                     304    311
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FK4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FK4)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MTNW_BACCR | Q819E8)
molecular function
    GO:0043715    2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity    Catalysis of the reaction: 2,3-diketo-5-methylthiopentyl-1-phosphate = H+ + 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate. 2,3-diketo-5-methylthiopentyl-1-phosphate is also known as DK-MTP-1-P, and 2-hydroxy 3-keto-5-methylthiopentenyl-1-phosphate as HK-MTPenyl-1-P.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016984    ribulose-bisphosphate carboxylase activity    Catalysis of the reaction: D-ribulose 1,5-bisphosphate + CO2 + H2O = 2 3-phospho-D-glycerate.
biological process
    GO:0019284    L-methionine salvage from S-adenosylmethionine    The chemical reactions and pathways resulting in the formation of L-methionine from S-adenosylmethionine.
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0015977    carbon fixation    A metabolic process in which carbon (usually derived from carbon dioxide) is incorporated into organic compounds (usually carbohydrates).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

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